Spectronaut® 19: Unlock Your Data’s True Story

Spectronaut® 19: Unlock Your Data’s True Story

Seminar Recordings

Spectronaut 19 Provides Major Improvement for Library-free Analysis

Single-Shot DIA Proteome Analysis: the New Gold Standard for Quantitative Proteomics

Tejas Gandhi (Biognosys)

Over the past years, directDIA has become the most popular workflow for processing DIA data using Spectronaut. With Spectronaut 19, we further improved our algorithms and deep learning models that power directDIA. As a result, the new version provides a major improvement in identification, quantification and computational performance of directDIA.

Josh Coon (University of Wisconsin-Madison)

In this presentation I will discuss my personal perspective on the evolution of protein quantification technologies over the past two decades. With the ultimate desire to achieve full proteome level quantification of hundreds to thousands of biological samples, this goal seemed distant even five years ago. Today, through rapid advances in both mass analyzer technology and DIA spectral analysis software, we are well on our way to achieving this ultimate goal. Here I will provide several examples of this powerful combination including: rapid global phosphoproteome profiling, 30-minute near complete human proteome analysis, deep proteome profiling for the discovery of mRNA editing, and very high throughput liver proteomics for quantitative trait loci mapping.

Short Bio Tejas Gandhi:

Tejas graduated as a computer scientist from Mankato State University, Minnesota. For his PhD, he joined the Membrane Enzymology group as a Bioinformatician at University of Groningen and received his degree in 2011. After that, Tejas joined Biognosys as one of its early employees. As Head of Bioinformatics, Tejas is passionate about software development for proteomics technology which provides both high quality and high novelty.

Short Bio Josh Coon:

Joshua J. Coon is a Professor of Chemistry and Biomolecular Chemistry at the University of Wisconsin-Madison and the Thomas and Margaret Pyle Chair at the Morgridge Institute for Research. Coon earned his B.S. degree at Central Michigan University and received his Ph.D. at the University of Florida in 2002. At Florida, Coon studied ambient ionization processes under the guidance of Professor Willard Harrison. From 2003 to 2005 he was an NIH postdoctoral fellow with Professor Donald Hunt at the University of Virginia. During his time at Virginia he, with Hunt and John Syka, coinvented electron transfer dissociation (ETD). Coon’s research program at Wisconsin is focused on all aspects of biomolecular mass spectrometry. Major technical innovations by Coon and his team include coupling of ETD and gas chromatography with the Orbitrap mass spectrometer, development of Parallel Reaction Monitoring (PRM), the use of multiple proteases for deep sequencing of proteomes, integrated multi-omics, and the development of new technologies for coupling cryo-EM with mass spectrometry.

Towards High-dimensional Phosphoproteomics with Data-independent Acquisition and µPhos

Denys Oliinyk (Jena University Hospital)

Mass spectrometry (MS)-based phosphoproteomics has transformed cell signalling research by probing many thousands of phosphorylation sites within the human proteome. However, most studies still investigate only a few conditions because established protocols require millions of cells to achieve the desired coverage of key signalling pathways, entailing labour-intensive workflows and high costs. Addressing this, we recently integrated trapped ion mobility – MS with µPhos, scalable and sensitive platform for phosphopeptide enrichment, which minimizes processing volumes and transfer steps to allow lossless processing of 96-well cell culture plates or other input-limited samples with one day. In combination with diaPASEF, we quantify >10,000 class I phosphosites with excellent reproducibility (median CV < 15%) and data completeness (>99%) from 10 µg protein starting amount, which equates the protein mass of cells cultured in a 96-well format (~40,000 HeLa cells). We further made µPhos protocol compatible with automatization on AssayMap Bravo robotic system. We take advantage of µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain, we reveal distinct kinase activities in subregions of the hippocampal formation.

Short Bio Denys Oliinyk:

Denys Oliinyk completed is masters with Henning Urlaub at the Max Plank Institute for Multidisciplinary Sciences in Göttingen, Germany. Since 2021 has been a PhD Student at University Hospital Jena with Florian Meier and is interested in functional phosphoproteomics. Denys is also an Amgen Scholar and an ASMS 2024 Graduate Student Awards recipient.

Back to Resources overview


    Close banner

    New: Spectronaut® 19

    Unlock Your Data's True Story

    New: Spectronaut® 19

    Unlock Your Data's True Story

    Learn More